I'm in process of making a new iOS tweak. I grabbed iOS Headers https://github.com/MP0w/iOS-Headers. Later on I figured out another repository on Github named iOS Runtime Headers https://github.com/nst/iOS-Runtime-Headers
Now i'm confused. What is the difference between these two?
It's hard to say what the differences are. They are both sets of headers generated with runtime introspection. The first one says it's headers both public and private.
Just so everybody understands, both links point to sets of headers that give you access to private OS APIs. Using these will get you rejected from the app store. They're only really useful for developing apps for the developer's personal use, or for jailbroken development.